AMBER: how to create 2'-5' RNA

From: <>
Date: Fri, 23 Jun 2006 17:13:57 -0400

Dear all,
I am attempting to model some 2'-5' RNA molecules (using Amber 8).  In leap I
edited RC, RC5, RG, RG5, etc not to have HO'2 atoms but to have HO'3 atoms.  I
saved these prep files changed them by hand to have the correct charges and atom
types for O3', O2', C3', C2', and HO'3.
I then modified my pdb file, loaded my prep residues, then read my pdb file in.
 As a result leap doesn't seem to know what to do with the connections...
basically I get a wound up structure looking like a crazy spool of yarn.
I have attached a copy of my pdb file and one of my residues.
Thanks in advance,
Seth Lilavivat
Georgia Institute of Technology

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Received on Sun Jun 25 2006 - 06:07:20 PDT
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